Index

_

__init__() (core.preprocessing.stainnorm.StainNormalizer method) (core.preprocessing.tissuemask.UNetTissueMaskExtractor method) (core.registration.cpd.CPD method)

A

adjust_gamma() (in module core.preprocessing.preprocessing) ALPHA (core.config.VisualizationParams attribute) apply_affine_transformation() (core.registration.rigid.Trimorph static method) (in module core.utils.util) apply_deformation_field() (in module core.registration.nonrigid)

apply_deformation_to_points() (in module core.utils.util) apply_displacement_field() (in module core.utils.mha_wsi) (in module core.utils.util) apply_displacement_field_to_points() (in module core.evaluation.evaluation) apply_padding_landmarks() (in module core.preprocessing.padding) array_to_vips() (in module core.utils.mha_wsi)

B

build_reference_coordinate_system() (in module core.registration.nonrigid)

C

calculate_pad_value() (in module core.preprocessing.padding) calculate_resample_size() (in module core.utils.util) combine_deformation() (in module core.utils.util) compute_center_of_mass() (core.registration.rigid.Trimorph static method) (in module core.utils.util) compute_deformation_and_apply() (in module core.registration.nonrigid) compute_normalized_cross_correlation() (in module core.registration.nonrigid) compute_smoothness_regularization() (in module core.registration.nonrigid) compute_svd() (core.preprocessing.stainnorm.StainNormalizer method) convert_4x4_to_3x3_transform() (in module core.registration.registration) convert_image_to_tensor() (in module core.registration.nonrigid) convert_pytorch_checkpoint() (core.preprocessing.tissuemask.UNetTissueMaskExtractor static method) (in module core.utils.util) core module core.evaluation.evaluation module core.preprocessing.nuclei_analysis module core.preprocessing.padding module core.preprocessing.preprocessing module core.preprocessing.stainnorm module core.preprocessing.tissuemask module core.registration.cpd module

core.registration.nonrigid module core.registration.registration module core.registration.rigid module core.utils.imports module core.utils.mha_wsi module core.utils.util module core.visualization.visualization module CPD (class in core.registration.cpd) create_deform() (in module core.utils.util) create_deformation_field() (in module core.utils.util) create_detailed_nuclei_plot_with_colormaps() (in module core.visualization.visualization) create_displacement_field() (in module core.registration.registration) create_displacement_field_for_wsi() (in module core.utils.util) create_method_comparison_plot() (in module core.visualization.visualization) create_multiscale_representation() (in module core.registration.nonrigid) create_nonrigid_mha() (in module core.utils.util) create_nuclei_dataframe_from_points() (in module core.preprocessing.nuclei_analysis) create_nuclei_overlay_plot() (in module core.visualization.visualization) create_pyramid() (in module core.utils.util) create_registration_comparison_plot() (in module core.visualization.visualization)

D

deform_conversion() (in module core.utils.util) detect_nuclei_patch_watershed() (in module core.preprocessing.nuclei_analysis)

dice() (in module core.utils.util) DISPLACEMENT_SIGMA (core.config.RegistrationParams attribute)

E

elastic_image_registration() (in module core.registration.nonrigid) evaluate_nonrigid_registration() (in module core.evaluation.evaluation) evaluate_registration_tre() (in module core.evaluation.evaluation) extract() (core.preprocessing.tissuemask.FlorenceTissueMaskExtractor method) extract_corresponding_tiles() (in module core.registration.rigid)

extract_H_E() (core.preprocessing.stainnorm.StainNormalizer method) extract_masks() (core.preprocessing.tissuemask.UNetTissueMaskExtractor method) extract_nuclei_points() (in module core.preprocessing.nuclei_analysis) extract_patches_from_wsi() (in module core.preprocessing.nuclei_analysis) extract_tissue_masks() (in module core.preprocessing.preprocessing)

F

FIGURE_HEIGHT (core.config.VisualizationParams attribute) FIGURE_WIDTH (core.config.VisualizationParams attribute) find_mutual_nearest_neighbors() (in module core.registration.registration)

find_scale() (in module core.utils.util) find_stain_vectors() (core.preprocessing.stainnorm.StainNormalizer method) FIXED_COLOR (core.config.VisualizationParams attribute) FlorenceTissueMaskExtractor (class in core.preprocessing.tissuemask)

G

gamma_corrections() (in module core.preprocessing.preprocessing) (in module core.utils.util) gaussian_filter() (in module core.utils.util)

gaussian_smoothing() (in module core.registration.nonrigid) get_image_shape() (in module core.utils.mha_wsi) get_transformation_matrix() (core.registration.rigid.ShapeAwarePointSetRegistration method)

I

initialize_deformation_field() (in module core.registration.nonrigid)

INTERPOLATION_METHOD (core.config.RegistrationParams attribute)

L

load_evaluation_landmarks() (in module core.evaluation.evaluation) load_image() (in module core.utils.util) load_image_as_grayscale() (in module core.utils.util) load_landmark_points() (in module core.evaluation.evaluation) load_landmarks() (in module core.utils.util)

load_landmarks_no_header() (in module core.utils.util) load_mha_displacement() (in module core.utils.mha_wsi) load_nuclei_coordinates() (in module core.preprocessing.nuclei_analysis) load_slide() (in module core.preprocessing.preprocessing) load_wsi_images() (in module core.preprocessing.preprocessing)

M

matchpoints() (in module core.utils.util) matrix_df() (in module core.utils.util) matrix_mha() (in module core.utils.util) MAX_DISPLACEMENT (core.config.RegistrationParams attribute) MNN_SAMPLE_SIZE (core.config.RegistrationParams attribute) module core core.evaluation.evaluation core.preprocessing.nuclei_analysis core.preprocessing.padding core.preprocessing.preprocessing core.preprocessing.stainnorm core.preprocessing.tissuemask core.registration.cpd core.registration.nonrigid core.registration.registration core.registration.rigid core.utils.imports core.utils.mha_wsi core.utils.util core.visualization.visualization

MOVING_COLOR (core.config.VisualizationParams attribute) mse() (in module core.utils.util)

N

ngf_metric() (in module core.evaluation.evaluation)

NONRIGID_COLOR (core.config.VisualizationParams attribute) normalize() (in module core.utils.util)

P

pad_image_src() (in module core.preprocessing.padding) pad_images() (in module core.preprocessing.padding) pad_images_np() (in module core.preprocessing.preprocessing) pad_landmarks() (in module core.preprocessing.padding) (in module core.utils.util) pad_single() (in module core.preprocessing.preprocessing) pad_to_same_size() (in module core.preprocessing.preprocessing) perform_cpd_registration() (in module core.registration.registration) perform_icp_registration() (in module core.registration.registration) perform_rigid_registration() (in module core.registration.registration) perform_shape_aware_registration() (in module core.registration.registration) (in module core.registration.rigid) phase_correlation() (in module core.utils.util) play_animation() (core.registration.cpd.CPD method)

plot_landmarks() (in module core.utils.util) POINT_SIZE_LARGE (core.config.VisualizationParams attribute) POINT_SIZE_MEDIUM (core.config.VisualizationParams attribute) POINT_SIZE_SMALL (core.config.VisualizationParams attribute) post_processing_mask() (core.preprocessing.tissuemask.UNetTissueMaskExtractor static method) prealignment() (core.registration.rigid.Trimorph method) prepare_image_tensors() (in module core.registration.nonrigid) preprocess_images() (in module core.preprocessing.preprocessing) print_rtre() (in module core.utils.util) process() (core.preprocessing.stainnorm.StainNormalizer method) process_fixed_patch() (in module core.preprocessing.nuclei_analysis) process_moving_patch() (in module core.preprocessing.nuclei_analysis) process_nuclei_in_patches() (in module core.preprocessing.nuclei_analysis) process_nuclei_patch() (in module core.preprocessing.preprocessing)

R

read_image() (core.preprocessing.stainnorm.StainNormalizer method) recreate_image() (core.preprocessing.stainnorm.StainNormalizer method) register() (core.registration.rigid.ShapeAwarePointSetRegistration method) (core.registration.rigid.XFeatReg method) register_wsi_with_fine_tuning() (in module core.registration.rigid) register_wsi_with_mha() (in module core.utils.mha_wsi) RegistrationParams (class in core.config) remove_padding() (in module core.preprocessing.padding) remove_transparent_pixels() (core.preprocessing.stainnorm.StainNormalizer method) resample() (in module core.utils.util)

resample_both() (in module core.utils.util) resample_displacement_field() (in module core.utils.util) resize_and_compute_translation() (in module core.preprocessing.preprocessing) resize_displacement_field() (in module core.utils.mha_wsi) rgb_to_od() (core.preprocessing.stainnorm.StainNormalizer method) RIGID_COLOR (core.config.VisualizationParams attribute) rigid_registration() (in module core.registration.rigid) rotate_point() (in module core.utils.util) round_up_to_odd() (in module core.utils.util) rtre() (in module core.evaluation.evaluation) (in module core.utils.util)

S

save_displacement_as_mha() (in module core.utils.mha_wsi) save_landmarks() (in module core.utils.util) save_nuclei_data_to_csv() (in module core.preprocessing.nuclei_analysis) scale_coordinates() (in module core.utils.util) scale_deformation_field() (in module core.registration.nonrigid) scale_tensor_to_dimensions() (in module core.registration.nonrigid) scale_transformation_matrix() (in module core.preprocessing.preprocessing) (in module core.utils.util) separate_stains() (core.preprocessing.stainnorm.StainNormalizer method)

setup_bokeh_notebook() (in module core.visualization.visualization) ShapeAwarePointSetRegistration (class in core.registration.rigid) show_plot() (in module core.visualization.visualization) skip_subsample() (in module core.utils.util) solve_affine() (core.registration.cpd.CPD method) solve_nonrigid() (core.registration.cpd.CPD method) solve_rigid() (core.registration.cpd.CPD method) sort_coordinates() (in module core.utils.util) StainNormalizer (class in core.preprocessing.stainnorm) subsample_nuclei() (in module core.preprocessing.nuclei_analysis)

T

tensor_to_rgb_numpy() (in module core.utils.util) to_image() (in module core.utils.util) transform_landmarks() (in module core.utils.util)

transform_points_homogeneous() (in module core.evaluation.evaluation) tre() (in module core.evaluation.evaluation) (in module core.utils.util) Trimorph (class in core.registration.rigid)

U

UNetTissueMaskExtractor (class in core.preprocessing.tissuemask)

V

vips_to_array() (in module core.utils.mha_wsi) VisualizationParams (class in core.config) visualize_cluster_alignment() (in module core.visualization.visualization)

visualize_overlays() (in module core.visualization.visualization) visualize_patches() (in module core.visualization.visualization) visualize_shape_aware_registration() (in module core.visualization.visualization) visualize_transformed_image() (in module core.visualization.visualization)

W

warp_corners_and_draw_matches() (core.registration.rigid.XFeatReg method)

warp_image() (in module core.utils.util)

X

XFeatReg (class in core.registration.rigid)